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ensembl-gh-mirror
ensembl-hive
Commits
7839833b
Commit
7839833b
authored
Jul 03, 2018
by
Brandon Walts
Browse files
Merge branch 'version/1.9' into version/2.0
parents
1bcdc85a
02838fc6
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modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm
modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm
+12
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modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm
View file @
7839833b
...
...
@@ -149,11 +149,21 @@ sub check_worker_is_alive_and_mine {
my
$wpid
=
$worker
->
process_id
();
my
$this_user
=
$ENV
{'
USER
'};
my
$cmd
=
qq{bjobs
$wpid
-u $this_user
2>&1 | grep -v 'not found' | grep -v JOBID | grep -v EXIT
}
;
my
$cmd
=
qq{bjobs -u $this_user
$wpid 2>&1
}
;
my
@bjobs_out
=
qx/$cmd/
;
# warn "LSF::check_worker_is_alive_and_mine() running cmd:\n\t$cmd\n";
my
$is_alive_and_mine
=
qx/$cmd/
;
my
$is_alive_and_mine
=
0
;
foreach
my
$bjobs_line
(
@bjobs_out
)
{
unless
(
$bjobs_line
=~
/JOBID|DONE|EXIT/
)
{
# *SUSP, UNKWN, and ZOMBI are "alive" for the purposes of this call
# which is typically used to see if the process can be killed.
# Can't search for line containing the job id, since it may be
# formatted differently in bjob output than in $worker->process_id()
# (e.g. for array jobs), so we exclude the header by excluding "JOBID"
$is_alive_and_mine
=
1
;
}
}
return
$is_alive_and_mine
;
}
...
...
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